15.map-fda-compounds.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Read FDA compounds\n",
    "\n",
    "https://github.com/greenelab/circadian-clock-modulators/issues/1\n",
    "\n",
    "> The SCREENWELL FDA-approved drug library V2 containing 741 compounds was purchased from Enzo Life Sciences (Hayashi Kasei Co., Ltd.), and the International Drug Collection (IDC) containing 311 compounds was purchased from MicroSource Discovery Systems, Inc. (Namiki Shoji Co., Ltd.)."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "import logging\n",
    "\n",
    "import pandas\n",
    "import requests_cache\n",
    "\n",
    "from utils.pubchem import query_pubchem_for_drugbank"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "requests_cache.install_cache(cache_name=\"requests-cache\", allowable_codes=[200, 404])"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Read tamai screen results"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>compound_name</th>\n",
       "      <th>compound_set</th>\n",
       "      <th>concentration</th>\n",
       "      <th>period_before</th>\n",
       "      <th>period_change</th>\n",
       "      <th>plate</th>\n",
       "      <th>notes</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>Clindamycin·HCl</td>\n",
       "      <td>fda</td>\n",
       "      <td>1 uM</td>\n",
       "      <td>21.5</td>\n",
       "      <td>0.02917</td>\n",
       "      <td>1</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>Felbamate</td>\n",
       "      <td>fda</td>\n",
       "      <td>1 uM</td>\n",
       "      <td>21.7</td>\n",
       "      <td>0.06250</td>\n",
       "      <td>1</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "     compound_name compound_set concentration  period_before  period_change  \\\n",
       "0  Clindamycin·HCl          fda          1 uM           21.5        0.02917   \n",
       "1        Felbamate          fda          1 uM           21.7        0.06250   \n",
       "\n",
       "   plate notes  \n",
       "0      1   NaN  \n",
       "1      1   NaN  "
      ]
     },
     "execution_count": 3,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "screen_df = pandas.read_table(\"data/tamai-screen/combined-results.tsv\")\n",
    "screen_df.head(2)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Read Screen-Well compounds\n",
    "\n",
    "The spreadsheet contains chemical structures in `mrv` format (ChemAxon MRV format, [Marvin Document](https://docs.chemaxon.com/display/docs/Marvin_Documents_-_MRV.html)). This format appears to be propreitary / not well supported, so map via other fields instead."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
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       "\n",
       "    .dataframe tbody tr th {\n",
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       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>Hash</th>\n",
       "      <th>StructureStringLength</th>\n",
       "      <th>StructureStringFormat</th>\n",
       "      <th>StructureString</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>50A647B589F94DEB7D0CBA1EAE819980</td>\n",
       "      <td>1</td>\n",
       "      <td>mrv</td>\n",
       "      <td>JChemExcelFgsAAB+LCAAAAAAABADtvQdgHEmWJSYvbcp7...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>C725614FF6722BF574DB2EE705636395</td>\n",
       "      <td>1</td>\n",
       "      <td>mrv</td>\n",
       "      <td>JChemExcelogYAAB+LCAAAAAAABADtvQdgHEmWJSYvbcp7...</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "                               Hash  StructureStringLength  \\\n",
       "0  50A647B589F94DEB7D0CBA1EAE819980                      1   \n",
       "1  C725614FF6722BF574DB2EE705636395                      1   \n",
       "\n",
       "  StructureStringFormat                                    StructureString  \n",
       "0                   mrv  JChemExcelFgsAAB+LCAAAAAAABADtvQdgHEmWJSYvbcp7...  \n",
       "1                   mrv  JChemExcelogYAAB+LCAAAAAAABADtvQdgHEmWJSYvbcp7...  "
      ]
     },
     "execution_count": 4,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# mrv (ChemAxon MRV format)\n",
    "xlsx_path = \"data/compounds/BML-2843_v. 1.4_Rev. 18Dec19_StructureFile.xlsx\"\n",
    "structure_df = pandas.read_excel(xlsx_path, sheet_name=0)\n",
    "structure_df.head(2)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
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       "\n",
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       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>screenwell_structure</th>\n",
       "      <th>screenwell_smiles</th>\n",
       "      <th>screenwell_iupac</th>\n",
       "      <th>screenwell_plate_location</th>\n",
       "      <th>screenwell_catalog_number</th>\n",
       "      <th>screenwell_name</th>\n",
       "      <th>screenwell_cas</th>\n",
       "      <th>screenwell_mw</th>\n",
       "      <th>screenwell_concentration</th>\n",
       "      <th>screenwell_solvent</th>\n",
       "      <th>screenwell_plate_number</th>\n",
       "      <th>screenwell_plate_description</th>\n",
       "      <th>screenwell_approval_year</th>\n",
       "      <th>screenwell_indication</th>\n",
       "      <th>screenwell_mechanism_of_action</th>\n",
       "      <th>screenwell_notes/toxicity</th>\n",
       "      <th>screenwell_plate_part_number</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>&lt;NA&gt;</td>\n",
       "      <td>CCC[C@@H]1CC(N(C1)C)C(=O)N[C@@H](C2[C@@H]([C@H...</td>\n",
       "      <td>(4R)-N-[(1S,2S)-2-chloro-1-[(3R,4R,6R)-3,4,5-t...</td>\n",
       "      <td>1-A02</td>\n",
       "      <td>A190</td>\n",
       "      <td>Clindamycin · HCl</td>\n",
       "      <td>21462-39-5</td>\n",
       "      <td>461.4</td>\n",
       "      <td>10 mM</td>\n",
       "      <td>DMSO</td>\n",
       "      <td>1</td>\n",
       "      <td>FDA Library II</td>\n",
       "      <td>1970</td>\n",
       "      <td>Antibiotic</td>\n",
       "      <td>Systemic/vaginal clindamycin inhibits protein ...</td>\n",
       "      <td>Side effects include: diarrhea, pseudomembrano...</td>\n",
       "      <td>2843</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>&lt;NA&gt;</td>\n",
       "      <td>C1=CC=C(C=C1)C(COC(=O)N)COC(=O)N</td>\n",
       "      <td>(3-carbamoyloxy-2-phenylpropyl) carbamate</td>\n",
       "      <td>1-A03</td>\n",
       "      <td>DL567</td>\n",
       "      <td>Felbamate</td>\n",
       "      <td>25451-15-4</td>\n",
       "      <td>238.2</td>\n",
       "      <td>10 mM</td>\n",
       "      <td>DMSO</td>\n",
       "      <td>1</td>\n",
       "      <td>FDA Library II</td>\n",
       "      <td>1993</td>\n",
       "      <td>Anticonvulsant</td>\n",
       "      <td>Precise mechanism unknown; It has an effect on...</td>\n",
       "      <td>Adverse reactions include decreased appetite, ...</td>\n",
       "      <td>2843</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "   screenwell_structure                                  screenwell_smiles  \\\n",
       "0                  <NA>  CCC[C@@H]1CC(N(C1)C)C(=O)N[C@@H](C2[C@@H]([C@H...   \n",
       "1                  <NA>                   C1=CC=C(C=C1)C(COC(=O)N)COC(=O)N   \n",
       "\n",
       "                                    screenwell_iupac  \\\n",
       "0  (4R)-N-[(1S,2S)-2-chloro-1-[(3R,4R,6R)-3,4,5-t...   \n",
       "1          (3-carbamoyloxy-2-phenylpropyl) carbamate   \n",
       "\n",
       "  screenwell_plate_location screenwell_catalog_number    screenwell_name  \\\n",
       "0                     1-A02                      A190  Clindamycin · HCl   \n",
       "1                     1-A03                     DL567          Felbamate   \n",
       "\n",
       "  screenwell_cas screenwell_mw screenwell_concentration screenwell_solvent  \\\n",
       "0     21462-39-5         461.4                    10 mM               DMSO   \n",
       "1     25451-15-4         238.2                    10 mM               DMSO   \n",
       "\n",
       "   screenwell_plate_number screenwell_plate_description  \\\n",
       "0                        1               FDA Library II   \n",
       "1                        1               FDA Library II   \n",
       "\n",
       "  screenwell_approval_year screenwell_indication  \\\n",
       "0                     1970            Antibiotic   \n",
       "1                     1993        Anticonvulsant   \n",
       "\n",
       "                      screenwell_mechanism_of_action  \\\n",
       "0  Systemic/vaginal clindamycin inhibits protein ...   \n",
       "1  Precise mechanism unknown; It has an effect on...   \n",
       "\n",
       "                           screenwell_notes/toxicity  \\\n",
       "0  Side effects include: diarrhea, pseudomembrano...   \n",
       "1  Adverse reactions include decreased appetite, ...   \n",
       "\n",
       "   screenwell_plate_part_number  \n",
       "0                          2843  \n",
       "1                          2843  "
      ]
     },
     "execution_count": 5,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "screenwell_df = pandas.read_excel(xlsx_path, sheet_name=1).add_prefix(\"screenwell_\").convert_dtypes()\n",
    "# fix messy column names\n",
    "screenwell_df.columns = screenwell_df.columns.str.strip().str.lower().str.replace(\" \", \"_\")\n",
    "# remove blank rows\n",
    "screenwell_df = screenwell_df.query(\"screenwell_name != 'Blank'\")\n",
    "screenwell_df.head(2)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "152"
      ]
     },
     "execution_count": 6,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# Number of compound names in the screen where exact text match fails\n",
    "screen_names = sorted(screen_df.query(\"compound_set == 'fda'\").compound_name.unique())\n",
    "len(set(screen_names) - set(screenwell_df.screenwell_name))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "WARNING:root:IUPAC lookup failed for Ranitidine·HCl\n",
      "WARNING:root:IUPAC lookup failed for Cefepime·2HCl Hydrate\n",
      "WARNING:root:IUPAC lookup failed for Terazosin·HCl\n",
      "WARNING:root:IUPAC lookup failed for Ceftizoxim·Na\n",
      "WARNING:root:IUPAC lookup failed for Ceftriaxone·Na\n",
      "WARNING:root:IUPAC lookup failed for Cefuroxime·Na\n",
      "WARNING:root:IUPAC lookup failed for Dantrolene . sodium\n",
      "WARNING:root:IUPAC lookup failed for Demeclocycline·HCl\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "CPU times: user 3.54 s, sys: 216 ms, total: 3.75 s\n",
      "Wall time: 39.5 s\n"
     ]
    },
    {
     "data": {
      "text/plain": [
       "764"
      ]
     },
     "execution_count": 7,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "%%time\n",
    "rows = []\n",
    "for screenwell in screenwell_df.itertuples():\n",
    "    for by, compound_name in [\n",
    "            (\"name\", screenwell.screenwell_iupac),\n",
    "            (\"smiles\", screenwell.screenwell_smiles),\n",
    "            (\"name\", screenwell.screenwell_name),\n",
    "        ]:\n",
    "        row = query_pubchem_for_drugbank(compound_name, by=by)\n",
    "        if row:\n",
    "            break\n",
    "    else:\n",
    "        logging.warning(f\"IUPAC lookup failed for {screenwell.screenwell_name}\")\n",
    "        continue\n",
    "    row[\"screenwell_name\"] = screenwell.screenwell_name\n",
    "    rows.append(row)\n",
    "len(rows)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
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       "\n",
       "    .dataframe tbody tr th {\n",
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       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>screenwell_name</th>\n",
       "      <th>screenwell_catalog_number</th>\n",
       "      <th>screenwell_plate_location</th>\n",
       "      <th>screenwell_smiles</th>\n",
       "      <th>screenwell_iupac</th>\n",
       "      <th>query_compound</th>\n",
       "      <th>pubchem_cid</th>\n",
       "      <th>drugbank_id</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>Clindamycin · HCl</td>\n",
       "      <td>A190</td>\n",
       "      <td>1-A02</td>\n",
       "      <td>CCC[C@@H]1CC(N(C1)C)C(=O)N[C@@H](C2[C@@H]([C@H...</td>\n",
       "      <td>(4R)-N-[(1S,2S)-2-chloro-1-[(3R,4R,6R)-3,4,5-t...</td>\n",
       "      <td>CCC[C@@H]1CC(N(C1)C)C(=O)N[C@@H](C2[C@@H]([C@H...</td>\n",
       "      <td>53384906</td>\n",
       "      <td>&lt;NA&gt;</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>Felbamate</td>\n",
       "      <td>DL567</td>\n",
       "      <td>1-A03</td>\n",
       "      <td>C1=CC=C(C=C1)C(COC(=O)N)COC(=O)N</td>\n",
       "      <td>(3-carbamoyloxy-2-phenylpropyl) carbamate</td>\n",
       "      <td>(3-carbamoyloxy-2-phenylpropyl) carbamate</td>\n",
       "      <td>3331</td>\n",
       "      <td>DB00949</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>Cyclosporin A</td>\n",
       "      <td>A195</td>\n",
       "      <td>1-A04</td>\n",
       "      <td>CC[C@H]1C(=O)N(CC(=O)N([C@H](C(=O)N[C@H](C(=O)...</td>\n",
       "      <td>(3S,6S,9S,12R,15S,18S,21S,24S,30S,33S)-30-ethy...</td>\n",
       "      <td>Cyclosporin A</td>\n",
       "      <td>5284373</td>\n",
       "      <td>DB00091</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>Donepezil·HCl</td>\n",
       "      <td>DL568</td>\n",
       "      <td>1-A05</td>\n",
       "      <td>COC1=C(C=C2C(=C1)CC(C2=O)CC3CCN(CC3)CC4=CC=CC=...</td>\n",
       "      <td>2-[(1-benzylpiperidin-4-yl)methyl]-5,6-dimetho...</td>\n",
       "      <td>2-[(1-benzylpiperidin-4-yl)methyl]-5,6-dimetho...</td>\n",
       "      <td>5741</td>\n",
       "      <td>&lt;NA&gt;</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>Lincomycin·HCl monohydrate</td>\n",
       "      <td>A240</td>\n",
       "      <td>1-A06</td>\n",
       "      <td>CCCC1CC(N(C1)C)C(=O)NC(C2C(C(C(C(O2)SC)O)O)O)C...</td>\n",
       "      <td>(2S,4R)-N-[(1R,2R)-2-hydroxy-1-[(2R,3R,4S,5R,6...</td>\n",
       "      <td>(2S,4R)-N-[(1R,2R)-2-hydroxy-1-[(2R,3R,4S,5R,6...</td>\n",
       "      <td>3000540</td>\n",
       "      <td>DB01627</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "              screenwell_name screenwell_catalog_number  \\\n",
       "0           Clindamycin · HCl                      A190   \n",
       "1                   Felbamate                     DL567   \n",
       "2               Cyclosporin A                      A195   \n",
       "3               Donepezil·HCl                     DL568   \n",
       "4  Lincomycin·HCl monohydrate                      A240   \n",
       "\n",
       "  screenwell_plate_location  \\\n",
       "0                     1-A02   \n",
       "1                     1-A03   \n",
       "2                     1-A04   \n",
       "3                     1-A05   \n",
       "4                     1-A06   \n",
       "\n",
       "                                   screenwell_smiles  \\\n",
       "0  CCC[C@@H]1CC(N(C1)C)C(=O)N[C@@H](C2[C@@H]([C@H...   \n",
       "1                   C1=CC=C(C=C1)C(COC(=O)N)COC(=O)N   \n",
       "2  CC[C@H]1C(=O)N(CC(=O)N([C@H](C(=O)N[C@H](C(=O)...   \n",
       "3  COC1=C(C=C2C(=C1)CC(C2=O)CC3CCN(CC3)CC4=CC=CC=...   \n",
       "4  CCCC1CC(N(C1)C)C(=O)NC(C2C(C(C(C(O2)SC)O)O)O)C...   \n",
       "\n",
       "                                    screenwell_iupac  \\\n",
       "0  (4R)-N-[(1S,2S)-2-chloro-1-[(3R,4R,6R)-3,4,5-t...   \n",
       "1          (3-carbamoyloxy-2-phenylpropyl) carbamate   \n",
       "2  (3S,6S,9S,12R,15S,18S,21S,24S,30S,33S)-30-ethy...   \n",
       "3  2-[(1-benzylpiperidin-4-yl)methyl]-5,6-dimetho...   \n",
       "4  (2S,4R)-N-[(1R,2R)-2-hydroxy-1-[(2R,3R,4S,5R,6...   \n",
       "\n",
       "                                      query_compound  pubchem_cid drugbank_id  \n",
       "0  CCC[C@@H]1CC(N(C1)C)C(=O)N[C@@H](C2[C@@H]([C@H...     53384906        <NA>  \n",
       "1          (3-carbamoyloxy-2-phenylpropyl) carbamate         3331     DB00949  \n",
       "2                                      Cyclosporin A      5284373     DB00091  \n",
       "3  2-[(1-benzylpiperidin-4-yl)methyl]-5,6-dimetho...         5741        <NA>  \n",
       "4  (2S,4R)-N-[(1R,2R)-2-hydroxy-1-[(2R,3R,4S,5R,6...      3000540     DB01627  "
      ]
     },
     "execution_count": 8,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "screenwell_map_df = (\n",
    "    screenwell_df\n",
    "    [[\"screenwell_name\", \"screenwell_catalog_number\", \"screenwell_plate_location\", \"screenwell_smiles\", \"screenwell_iupac\"]]\n",
    "    .merge(pandas.DataFrame(rows), how=\"left\")\n",
    "    .convert_dtypes()\n",
    ")\n",
    "screenwell_map_df.head(5)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "557 compounds mapped to pubchem via screenwell_iupac\n",
      "191 compounds mapped to pubchem via screenwell_smiles\n",
      "33 compounds mapped to pubchem via screenwell_name\n",
      "8 compounds failed to map to pubchem\n",
      "\n",
      "406 compounds mapped to DrugBank\n"
     ]
    }
   ],
   "source": [
    "print(f\"\"\"\n",
    "{(screenwell_map_df.query_compound == screenwell_map_df.screenwell_iupac).sum():,} compounds mapped to pubchem via screenwell_iupac\n",
    "{(screenwell_map_df.query_compound == screenwell_map_df.screenwell_smiles).sum():,} compounds mapped to pubchem via screenwell_smiles\n",
    "{(screenwell_map_df.query_compound == screenwell_map_df.screenwell_name).sum():,} compounds mapped to pubchem via screenwell_name\n",
    "{sum(screenwell_map_df.pubchem_cid.isna()):,} compounds failed to map to pubchem\n",
    "\n",
    "{sum(screenwell_map_df.drugbank_id.notna()):,} compounds mapped to DrugBank\n",
    "\"\"\".strip())"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>screenwell_name</th>\n",
       "      <th>screenwell_catalog_number</th>\n",
       "      <th>screenwell_plate_location</th>\n",
       "      <th>screenwell_smiles</th>\n",
       "      <th>screenwell_iupac</th>\n",
       "      <th>query_compound</th>\n",
       "      <th>pubchem_cid</th>\n",
       "      <th>drugbank_id</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>61</th>\n",
       "      <td>Ranitidine·HCl</td>\n",
       "      <td>AC766</td>\n",
       "      <td>1-G03</td>\n",
       "      <td>CN/C(=C/[N+](=O)[O-])/NCCSCC1=CC=C(O1)CN(C)C.Cl</td>\n",
       "      <td>(Z)-1-N'-[2-[[5-[(dimethylamino)methyl]furan-2...</td>\n",
       "      <td>&lt;NA&gt;</td>\n",
       "      <td>&lt;NA&gt;</td>\n",
       "      <td>&lt;NA&gt;</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>88</th>\n",
       "      <td>Cefepime·2HCl Hydrate</td>\n",
       "      <td>DL191</td>\n",
       "      <td>2-A10</td>\n",
       "      <td>[H+].C[N+]1(CCCC1)CC2=C(N3C(C(C3=O)NC(=O)/C(=N...</td>\n",
       "      <td>7-[[(2Z)-2-(2-amino-1,3-thiazol-4-yl)-2-methox...</td>\n",
       "      <td>&lt;NA&gt;</td>\n",
       "      <td>&lt;NA&gt;</td>\n",
       "      <td>&lt;NA&gt;</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>342</th>\n",
       "      <td>Terazosin·HCl</td>\n",
       "      <td>DL513</td>\n",
       "      <td>5-C05</td>\n",
       "      <td>COC1=C(C=C2C(=C1)C(=NC(=N2)N3CCN(CC3)C(=O)C4CC...</td>\n",
       "      <td>[4-(4-amino-6,7-dimethoxyquinazolin-2-yl)piper...</td>\n",
       "      <td>&lt;NA&gt;</td>\n",
       "      <td>&lt;NA&gt;</td>\n",
       "      <td>&lt;NA&gt;</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>449</th>\n",
       "      <td>Ceftizoxim·Na</td>\n",
       "      <td>AC3053</td>\n",
       "      <td>6-H03</td>\n",
       "      <td>CO/N=C(\\C1=CSC(=N1)N)/C(=O)N[C@H]2[C@@H]3N(C2=...</td>\n",
       "      <td>sodium;(6R,7R)-7-[[(2E)-2-(2-amino-1,3-thiazol...</td>\n",
       "      <td>&lt;NA&gt;</td>\n",
       "      <td>&lt;NA&gt;</td>\n",
       "      <td>&lt;NA&gt;</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>450</th>\n",
       "      <td>Ceftriaxone·Na</td>\n",
       "      <td>AC3054</td>\n",
       "      <td>6-H04</td>\n",
       "      <td>CN1C(=NC(=O)C(=O)N1)SCC2=C(N3[C@@H]([C@@H](C3=...</td>\n",
       "      <td>sodium;7-[[(2Z)-2-(2-amino-1,3-thiazol-4-yl)-2...</td>\n",
       "      <td>&lt;NA&gt;</td>\n",
       "      <td>&lt;NA&gt;</td>\n",
       "      <td>&lt;NA&gt;</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>452</th>\n",
       "      <td>Cefuroxime·Na</td>\n",
       "      <td>AC3056</td>\n",
       "      <td>6-H06</td>\n",
       "      <td>CO/N=C(\\C1=CC=CO1)/C(=O)N[C@H]2[C@@H]3N(C2=O)C...</td>\n",
       "      <td>sodium;(6R,7R)-3-(carbamoyloxymethyl)-7-[[(2E)...</td>\n",
       "      <td>&lt;NA&gt;</td>\n",
       "      <td>&lt;NA&gt;</td>\n",
       "      <td>&lt;NA&gt;</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>483</th>\n",
       "      <td>Dantrolene . sodium</td>\n",
       "      <td>550072</td>\n",
       "      <td>7-C10</td>\n",
       "      <td>C1C(=O)N=C(N1/N=C/C2=CC=C(O2)C3=CC=C(C=C3)[N+]...</td>\n",
       "      <td>sodium;3-[(E)-[5-(4-nitrophenyl)furan-2-yl]met...</td>\n",
       "      <td>&lt;NA&gt;</td>\n",
       "      <td>&lt;NA&gt;</td>\n",
       "      <td>&lt;NA&gt;</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>492</th>\n",
       "      <td>Demeclocycline·HCl</td>\n",
       "      <td>AC3083</td>\n",
       "      <td>7-D09</td>\n",
       "      <td>CN(C)[C@H]1[C@@H]2C[C@@H]3[C@@H](C4=C(C=CC(=C4...</td>\n",
       "      <td>(4S,4aS,5aS,6S,12aR)-7-chloro-4-(dimethylamino...</td>\n",
       "      <td>&lt;NA&gt;</td>\n",
       "      <td>&lt;NA&gt;</td>\n",
       "      <td>&lt;NA&gt;</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "           screenwell_name screenwell_catalog_number  \\\n",
       "61          Ranitidine·HCl                     AC766   \n",
       "88   Cefepime·2HCl Hydrate                     DL191   \n",
       "342          Terazosin·HCl                     DL513   \n",
       "449          Ceftizoxim·Na                    AC3053   \n",
       "450         Ceftriaxone·Na                    AC3054   \n",
       "452          Cefuroxime·Na                    AC3056   \n",
       "483    Dantrolene . sodium                    550072   \n",
       "492     Demeclocycline·HCl                    AC3083   \n",
       "\n",
       "    screenwell_plate_location  \\\n",
       "61                      1-G03   \n",
       "88                      2-A10   \n",
       "342                     5-C05   \n",
       "449                     6-H03   \n",
       "450                     6-H04   \n",
       "452                     6-H06   \n",
       "483                     7-C10   \n",
       "492                     7-D09   \n",
       "\n",
       "                                     screenwell_smiles  \\\n",
       "61     CN/C(=C/[N+](=O)[O-])/NCCSCC1=CC=C(O1)CN(C)C.Cl   \n",
       "88   [H+].C[N+]1(CCCC1)CC2=C(N3C(C(C3=O)NC(=O)/C(=N...   \n",
       "342  COC1=C(C=C2C(=C1)C(=NC(=N2)N3CCN(CC3)C(=O)C4CC...   \n",
       "449  CO/N=C(\\C1=CSC(=N1)N)/C(=O)N[C@H]2[C@@H]3N(C2=...   \n",
       "450  CN1C(=NC(=O)C(=O)N1)SCC2=C(N3[C@@H]([C@@H](C3=...   \n",
       "452  CO/N=C(\\C1=CC=CO1)/C(=O)N[C@H]2[C@@H]3N(C2=O)C...   \n",
       "483  C1C(=O)N=C(N1/N=C/C2=CC=C(O2)C3=CC=C(C=C3)[N+]...   \n",
       "492  CN(C)[C@H]1[C@@H]2C[C@@H]3[C@@H](C4=C(C=CC(=C4...   \n",
       "\n",
       "                                      screenwell_iupac query_compound  \\\n",
       "61   (Z)-1-N'-[2-[[5-[(dimethylamino)methyl]furan-2...           <NA>   \n",
       "88   7-[[(2Z)-2-(2-amino-1,3-thiazol-4-yl)-2-methox...           <NA>   \n",
       "342  [4-(4-amino-6,7-dimethoxyquinazolin-2-yl)piper...           <NA>   \n",
       "449  sodium;(6R,7R)-7-[[(2E)-2-(2-amino-1,3-thiazol...           <NA>   \n",
       "450  sodium;7-[[(2Z)-2-(2-amino-1,3-thiazol-4-yl)-2...           <NA>   \n",
       "452  sodium;(6R,7R)-3-(carbamoyloxymethyl)-7-[[(2E)...           <NA>   \n",
       "483  sodium;3-[(E)-[5-(4-nitrophenyl)furan-2-yl]met...           <NA>   \n",
       "492  (4S,4aS,5aS,6S,12aR)-7-chloro-4-(dimethylamino...           <NA>   \n",
       "\n",
       "     pubchem_cid drugbank_id  \n",
       "61          <NA>        <NA>  \n",
       "88          <NA>        <NA>  \n",
       "342         <NA>        <NA>  \n",
       "449         <NA>        <NA>  \n",
       "450         <NA>        <NA>  \n",
       "452         <NA>        <NA>  \n",
       "483         <NA>        <NA>  \n",
       "492         <NA>        <NA>  "
      ]
     },
     "execution_count": 10,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# Screen-Well compounds not mapped to PubChem\n",
    "screenwell_map_df[screenwell_map_df.pubchem_cid.isna()]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {},
   "outputs": [],
   "source": [
    "screenwell_map_df.to_csv(\"data/compounds/screenwell-to-pubchem.tsv\", sep=\"\\t\", index=False)"
   ]
  }
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